[English] 日本語
Yorodumi
- EMDB-13057: Structure of the AI-2 exporter family protein YdiK from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13057
TitleStructure of the AI-2 exporter family protein YdiK from E. coli
Map dataFinal single particle EM map
Sample
  • Complex: Pentameric YdiK
    • Protein or peptide: AI-2E member YdiK
Keywordscryo-EM / membrane protein / autoinducer-2 exporter / quorum sensing / pentamer / protein oligomerization / STRUCTURAL PROTEIN / AI-2E / transporter
Function / homologyTransmembrane protein TqsA-like / AI-2E family transporter / plasma membrane / Putative transport protein YdiK
Function and homology information
Biological speciesEscherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKhera R / Xie H
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: EMBO J / Year: 2022
Title: Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism.
Authors: Radhika Khera / Ahmad R Mehdipour / Jani R Bolla / Joerg Kahnt / Sonja Welsch / Ulrich Ermler / Cornelia Muenke / Carol V Robinson / Gerhard Hummer / Hao Xie / Hartmut Michel /
Abstract: Bacteria utilize small extracellular molecules to communicate in order to collectively coordinate their behaviors in response to the population density. Autoinducer-2 (AI-2), a universal molecule for ...Bacteria utilize small extracellular molecules to communicate in order to collectively coordinate their behaviors in response to the population density. Autoinducer-2 (AI-2), a universal molecule for both intra- and inter-species communication, is involved in the regulation of biofilm formation, virulence, motility, chemotaxis, and antibiotic resistance. While many studies have been devoted to understanding the biosynthesis and sensing of AI-2, very little information is available on its export. The protein TqsA from Escherichia coli, which belongs to the AI-2 exporter superfamily, has been shown to export AI-2. Here, we report the cryogenic electron microscopic structures of two AI-2 exporters (TqsA and YdiK) from E. coli at 3.35 Å and 2.80 Å resolutions, respectively. Our structures suggest that the AI-2 exporter exists as a homo-pentameric complex. In silico molecular docking and native mass spectrometry experiments were employed to demonstrate the interaction between AI-2 and TqsA, and the results highlight the functional importance of two helical hairpins in substrate binding. We propose that each monomer works as an independent functional unit utilizing an elevator-type transport mechanism.
History
DepositionJun 9, 2021-
Header (metadata) releaseMay 11, 2022-
Map releaseMay 11, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13057.png

Downloads & links

-
Map

FileDownload / File: emd_13057.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal single particle EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 240 pix.
= 265.92 Å		1.11 Å/pix.
x 240 pix.
= 265.92 Å		1.11 Å/pix.
x 240 pix.
= 265.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.108 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0177
Minimum - Maximum-0.030504791 - 0.090286806
Average (Standard dev.)0.00025902665 (±0.0031349561)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 265.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_13057_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map1

Fileemd_13057_half_map_1.map
AnnotationHalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map2

Fileemd_13057_half_map_2.map
AnnotationHalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Pentameric YdiK

EntireName: Pentameric YdiK
Components
  • Complex: Pentameric YdiK
    • Protein or peptide: AI-2E member YdiK

-
Supramolecule #1: Pentameric YdiK

SupramoleculeName: Pentameric YdiK / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 199 KDa

-
Macromolecule #1: AI-2E member YdiK

MacromoleculeName: AI-2E member YdiK / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 39.865891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVNVRQPRDV AQILLSVLFL AIMIVACLWI VQPFILGFAW AGTVVIATWP VLLRLQKIMF GRRSLAVLVM TLLLVMVFII PIALLVNSI VDGSGPLIKA ISSGDMTLPD LAWLNTIPVI GAKLYAGWHN LLDMGGTAIM AKVRPYIGTT TTWFVGQAAH I GRFMVHCA ...String:
MVNVRQPRDV AQILLSVLFL AIMIVACLWI VQPFILGFAW AGTVVIATWP VLLRLQKIMF GRRSLAVLVM TLLLVMVFII PIALLVNSI VDGSGPLIKA ISSGDMTLPD LAWLNTIPVI GAKLYAGWHN LLDMGGTAIM AKVRPYIGTT TTWFVGQAAH I GRFMVHCA LMLLFSALLY WRGEQVAQGI RHFATRLAGV RGDAAVLLAA QAIRAVALGV VVTALVQAVL GGIGLAVSGV PY ATLLTVL MILSCLVQLG PLPVLIPAII WLYWTGDTTW GTVLLVWSGV VGTLDNVIRP MLIRMGADLP LILILSGVIG GLI AFGMIG LFIGPVLLAV SWRLFAAWVE EVPPPTDQPE EILEELGEIE KPNK

UniProtKB: Putative transport protein YdiK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.8 mg/mL
BufferpH: 7.5 / Details: 50 mM Tris (pH 7.5), 150 mM NaCl and 0.006% GDN
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III / Details: blot time 4 s, blot force +20.
DetailsIts a membrane protein and for purification, glyco-diosgenin was used.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 7378 / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1222739
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 619311
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more